[BUG] Overflows in irls_solver and shape mismatch in _refit_without_outliers when using continuous variable
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Description
When using a continuous variable I get
ValueError: shape mismatch: value array of shape (228,77) could not be broadcast to indexing result of shape (228,7)
while running self.varm["LFC"][to_replace] = sub_dds.varm["LFC"] in _refit_without_outliers.
I also get overflow warnings from irls_solver.
- Setting 1
design_factors=['Batch','Condition']
continuous_factors=None
Works fine
- Setting 2
design_factors=['Batch', 'Age', 'Condition']
continuous_factors=None
Works fine (Refitting 29547 outliers, compared to 1567 in the previous setting, does this make sense?)
- Setting 3
design_factors=['Batch', 'Age', 'Condition']
continuous_factors=['Age']
Overflows in irls_solver (similar to Issue #169). To be precise, I do not get these in previous settings.
ValueError: shape mismatch: value array of shape (228,77) could not be broadcast to indexing result of shape (228,7)
(while running self.varm["LFC"][to_replace] = sub_dds.varm["LFC"] in _refit_without_outliers)
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the issue using the three design_factors and continuous_factors settings in the report, then inspect _refit_without_outliers where self.varm["LFC"] is assigned and irls_solver where the overflow warnings occur. Done means the continuous-variable case no longer raises the reported shape-mismatch error and the associated overflows are addressed.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100